MolNFT v1 · #65108 · protein
Crystal structure of glutaryl-CoA dehydrogenase from burkholderia pseudomallei with fragment 6421
3GNC: “Crystal structure of glutaryl-CoA dehydrogenase from burkholderia pseudomallei with fragment 6421”. X-ray diffraction, 2 ligands (QQQ, SO4), 19 pockets (best druggability 0.78). MolNFT v1 #65108 on GenesisL1: 3D structure, binding…
- PDB
- 3GNC
- Type
- protein
- Length
- 1,515 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutaryl-CoA dehydrogenase
- EC
- 1.3.99.7
- UniProt
- Q3JP94
- Ligands
- QQQ, SO4
- Pockets
- 19 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 380 | 57% helix, 15% strand | Q3JP94 |
| B | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 372 | 57% helix, 16% strand | Q3JP94 |
| C | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 383 | 54% helix, 14% strand | Q3JP94 |
| D | Glutaryl-CoA dehydrogenase (EC 1.3.99.7) | protein | 380 | 57% helix, 15% strand | Q3JP94 |
Ligands and binding sites
- QQQ · 1-(1-methylethyl)-1H-benzimidazole-2-sulfonic acid · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 957 | 0.78 | 0.80 | 83 | EPE |
| 2 | 851 | 0.78 | 0.81 | 77 | SO4, EPE |
| 3 | 956 | 0.76 | 0.78 | 83 | QQQ |
| 4 | 522 | 0.73 | 0.81 | 56 | QQQ |
| 5 | 637 | 0.73 | 0.80 | 52 | QQQ |
Interfaces
6 interfaces between chains.
- C–D · 2392 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2359 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 1245 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1160 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 212 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3GNC · Crystal structure of Glutaryl-COA dehydrogenase from Burkholderia Pseudomallei with… · the same entry in another collection · chain B against B, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q3JP94
- Elsewhere: RCSB PDB 3GNC · PDBe 3GNC · UniProt Q3JP94
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